Structure of PDB 6djt Chain A Binding Site BS02

Receptor Information

>6djt Chain A (length=298) Species: 2190 (Methanocaldococcus jannaschii)

HMIPEEIYKILRKQRYQIDGHTAVKLCGWVRKKMLEDKNCYKSKFYGIET
HRCIQCTPSVIWCQQNCIFCWRVSQIKEPKWEEPEVVYEKILAMHKRIIM
GYAGVLDRVGEKKFKEALEPKHVAISLSGEPTLYPYLDELIKIFHKNGFT
TFVVSNGILTDVIEKIEPTQLYISLDAYDLDSYRRICGGKKEYWESILNT
LDILKEKKRTCIRTTLIRGYNDDILKFVELYERADVHFIELKSYMHVRLK
KEDMLQHDEILKLAKMLDENSSYKLIDDSEDSRVALLQNENRKINPKL

Ligand information

• Ligand ID: FS0
• InChI: InChI=1S/2Fe.H2S.2S/h;;1H2;;/q;+1;;;/p-1
• InChIKey: ANRWZFUZKQVIEA-UHFFFAOYSA-M
• SMILES:
  CACTVS 3.385
  OpenEye OEToolkits 2.0.6: S[Fe]1S[Fe]S1
  ACDLabs 12.01: [Fe]1S[Fe](S1)S
• Formula: Fe2 H S3
• Name: FE2/S3 CLUSTER
• PDB chain: 6djt Chain A Residue 412

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6djt Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1.
• Resolution: 1.64 Å
• Binding residue (original residue number in PDB): C62 Q64 N65 C66 C69 G137
• Binding residue (residue number reindexed from 1): C63 Q65 N66 C67 C70 G129
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 4.1.3.44: tRNA 4-demethylwyosine synthase (AdoMet-dependent).

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0016829 lyase activity
• GO:0016833 oxo-acid-lyase activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0102521 tRNA-4-demethylwyosine synthase activity

Biological Process

• GO:0008033 tRNA processing

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6djt, PDBe:6djt, PDBj:6djt
• PDBsum: 6djt
• PubMed: 29792696
• UniProt: Q57705|TYW1_METJA S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase (Gene Name=taw1)